My labmates and I have been seeing a strange characteristic in post processing experiments for unrelated proteins and haven't worked out the pattern yet. We see a sharp dip in the calculated SAXS curve not evident in experimental data. In my case, I study a protein made of two globular domains (with crystal structures) separated by an 80aa linker with unknown structure and binding characteristics. Below I have two fits from EOM for one data set processed with or without an input PDB file. The data is from the NTD+linker construct so the PDB is for the NTD.

No PDB

With PDB

I've see this in CORAL as well. Clearly it has to do with the inclusion of a PDB file, but I've used the same file with data for full length constructs and only seen "the dip" occasionally. Like I said, my lab mates have seen it in their data for very different proteins as well.